Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattaaaatccttaacatttttcttttctctgttatatggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G39520.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G15180.1 (Glycine max), 3'ss of exon 8
gtaagtaattaaaatccttaacatttttcttttctctgttat--atggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcc---tgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG------------------------------------------------
  ||  | ||  | ||  ||| || | |||   ||  |   |  |       || |      | |  || |     | |||| | |   |  ||   |||| ||| ||| |||| |||||||||||||| ||||||||||| ||||||||||| |||                                                
-aaaaaagtttgagtcaataa-atctctctccccttagcccttcaaaaaaaatgttttt---ctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAGGTTGATACTGTACTTAATTTACATTATTTTTTGCTTCATCCTCTTTTC

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 8
-----gtaagt--aattaaaatccttaacatttttcttttctctgttatatggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG
       ||||  | | ||||    | ||   |   |  ||  |   | ||| || |   ||   |   ||  | |   || |  |  ||  ||     |||| ||| ||| |||| |||||||||||||| ||||||||||| ||||||||||| |||
gagaaaaaagttgagtaaaaaaatctcacccctcggtcctccataaaaaatgtttttctttcctgacattcattta---attcacatttaccgaa----tgatgcagTGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 8
gtaagtaattaaaatccttaacatttttcttttctctg--ttatatggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcc---tgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG
  ||  | ||  | ||  ||| || | |||   ||  |   |  |       || |      | |  || |     | |||| | |   |  ||   |||| ||| ||| |||| |||||||||||||| ||||||||||| ||||||||||| |||
-aaaaaagtttgagtcaataa-atctctctccccttagcccttcaaaaaaaatgttttt---ctttcctgacattcatttaattcacatttaccaaatgatgcagTGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAG

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S26_115V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------gtaagtaattaaaatccttaacatttt-tcttttctctgttatatggttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcctgat-----acagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG
                          || || ||    ||  |  |  || | |   | |  | || |    | |||  |   |    |   |||   | | | |||| ||||    |  ||     |||| ||| |||| ||||||||||| || |||||||||||||| ||||| ||||||
gtaagtcctgaagttgacatttggtttatgttatcttgattgtccattttctataactaccatatttttatatccttattttgata-gtgattcactga-attcaactcatgagtatcatatggatgacagTGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125284963|gb|EL299048.1|EL299048
EST:     GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTA                         CGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
genomic: GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTAgtaagtaatt ... cctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
EST: gi|86076547|gb|DR372304.1|DR372304
EST:     GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTA                         CGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
genomic: GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTAgtaagtaatt ... cctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
EST: gi|164014232|gb|ES126882.1|ES126882
EST:     GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTA                         CGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
genomic: GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTAgtaagtaatt ... cctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
EST: gi|86080003|gb|DR375760.1|DR375760
EST:     GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTA                         CGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA
genomic: GAGGACTTCTGCATCCGGATTCACAAAGACATGCTTAAACAATTCAAGTAgtaagtaatt ... cctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgctcaaaagcatcgctcatgaatacttaactaatgatctcctgatacagCGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAG
                                          tctcct  CT-rich tract
                          aatacttaactaat  TA-rich tract